formatting

[jalview.git] / src / jalview / jbgui / GStructureViewer.java

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 1b50ca8..2b99d2b 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -83,7 +83,7 @@ public class GStructureViewer extends JInternalFrame
         backGround_actionPerformed(actionEvent);
       }
     });
-    seqColour.setSelected(true);
+    seqColour.setSelected(false);
     seqColour.setText("By Sequence");
     seqColour.addActionListener(new ActionListener()
     {
@@ -164,6 +164,15 @@ public class GStructureViewer extends JInternalFrame
         buriedColour_actionPerformed(actionEvent);
       }
     });
+    purinePyrimidineColour.setText("Purine/Pyrimidine");
+    purinePyrimidineColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        purinePyrimidineColour_actionPerformed(actionEvent);
+      }
+    });
+
     userColour.setText("User Defined ...");
     userColour.addActionListener(new ActionListener()
     {
@@ -172,6 +181,16 @@ public class GStructureViewer extends JInternalFrame
         userColour_actionPerformed(actionEvent);
       }
     });
+    jmolColour.setSelected(false);
+    jmolColour.setText("Colour with Jmol");
+    jmolColour.setToolTipText("Let Jmol manage structure colours.");
+    jmolColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        jmolColour_actionPerformed(actionEvent);
+      }
+    });
     helpMenu.setText("Help");
     jmolHelp.setText("Jmol Help");
     jmolHelp.addActionListener(new ActionListener()
@@ -181,9 +200,20 @@ public class GStructureViewer extends JInternalFrame
         jmolHelp_actionPerformed(actionEvent);
       }
     });
+    alignStructs.setText("Align structures");
+    alignStructs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        alignStructs_actionPerformed(actionEvent);
+      }
+    });
+    jmolActionMenu.setText("Jmol");
     menuBar.add(fileMenu);
     menuBar.add(viewMenu);
     menuBar.add(colourMenu);
+    menuBar.add(jmolActionMenu);
+    jmolActionMenu.setVisible(false);
     menuBar.add(helpMenu);
     fileMenu.add(savemenu);
     fileMenu.add(viewMapping);
@@ -191,6 +221,7 @@ public class GStructureViewer extends JInternalFrame
     savemenu.add(png);
     savemenu.add(eps);
     viewMenu.add(chainMenu);
+
     colourMenu.add(seqColour);
     colourMenu.add(chainColour);
     colourMenu.add(chargeColour);
@@ -201,9 +232,34 @@ public class GStructureViewer extends JInternalFrame
     colourMenu.add(strandColour);
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
+    colourMenu.add(purinePyrimidineColour);
     colourMenu.add(userColour);
+    colourMenu.add(jmolColour);
     colourMenu.add(backGround);
+
+    colourButtons.add(seqColour);
+    colourButtons.add(chainColour);
+    colourButtons.add(chargeColour);
+    colourButtons.add(zappoColour);
+    colourButtons.add(taylorColour);
+    colourButtons.add(hydroColour);
+    colourButtons.add(helixColour);
+    colourButtons.add(strandColour);
+    colourButtons.add(turnColour);
+    colourButtons.add(buriedColour);
+    colourButtons.add(userColour);
+    colourButtons.add(jmolColour);
+
     helpMenu.add(jmolHelp);
+    jmolActionMenu.add(alignStructs);
+  }
+
+  protected void jmolColour_actionPerformed(ActionEvent actionEvent)
+  {
+  }
+
+  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+  {
   }
 
   JMenuBar menuBar = new JMenuBar();
@@ -220,37 +276,47 @@ public class GStructureViewer extends JInternalFrame
 
   JMenuItem viewMapping = new JMenuItem();
 
-  JMenu viewMenu = new JMenu();
+  protected JMenu viewMenu = new JMenu();
 
   protected JMenu chainMenu = new JMenu();
 
   JMenu jMenu1 = new JMenu();
 
-  JMenu colourMenu = new JMenu();
+  protected JMenu colourMenu = new JMenu();
+
+  protected JMenu jmolActionMenu = new JMenu();
+
+  protected JMenuItem alignStructs = new JMenuItem();
 
   JMenuItem backGround = new JMenuItem();
 
-  protected JCheckBoxMenuItem seqColour = new JCheckBoxMenuItem();
+  protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
 
-  JMenuItem chainColour = new JMenuItem();
+  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
 
-  JMenuItem chargeColour = new JMenuItem();
+  protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
 
-  JMenuItem zappoColour = new JMenuItem();
+  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
 
-  JMenuItem taylorColour = new JMenuItem();
+  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
 
-  JMenuItem hydroColour = new JMenuItem();
+  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 
-  JMenuItem strandColour = new JMenuItem();
+  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 
-  JMenuItem helixColour = new JMenuItem();
+  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
 
-  JMenuItem turnColour = new JMenuItem();
+  protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
 
-  JMenuItem buriedColour = new JMenuItem();
+  protected JRadioButtonMenuItem jmolColour = new JRadioButtonMenuItem();
 
-  JMenuItem userColour = new JMenuItem();
+  protected ButtonGroup colourButtons = new ButtonGroup();
 
   JMenu helpMenu = new JMenu();
 
@@ -326,6 +392,11 @@ public class GStructureViewer extends JInternalFrame
 
   }
 
+  public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {